Acquiring a YODA output file
This is the tutorial for how to export your data from the Bioscreen. Things you'll need are: A computer, duh! LibreOffice Bioscreen files Login to YODA (Not needed but recommended) And for right now until things are settled--Microsoft Excel So go to the Bioscreen and go to Files>Export Result. Save the .txt file from the Bioscreen. From here, go to any one of the computers in the lab that has LibreOffice. Ask Mark if you don't know which ones have it- you can also download and install it for free on any PC, Mac, or Linux, unless it has been locked down by IT. Currently the two laptops in the quipment corridor that drive the Bioscreen and the VictorX3, and the laptop by the black and white printer that drives the NanoDrop, and the Linux side of the desktop by the dissectors, should all have LibreOffice. If you have your own laptop you can install it there. Once you've found a computer that has the program, right click on your .txt and click "Open With", and open the file with LibreOffice Calc. It will ask you for a character set and a language. For the character set, leave it on "Unicode" and the language at "Default - English (USA)". For the separator options, click on "Separated by" and make sure that the boxes for "Merge delimiters" and and "Space" are checked. Then press OK to open the file. The first thing you should do is delete the column named "Blank" and you may have to delete the lowest row. The reason for this is it sometimes throws off YODA since the format is weird. In any case, look at the figure I have on the side if you're confused. THIS NORMALIZATION STEP IS OPTIONAL Then copy everything you have and paste it into a new sheet. From here, go to the cell in the 2nd column in the 3rd row (this would be called cell B2). Click on this cell and type up this formula: =Sheet1.C2-(MIN(Sheet1.C2:GT49)) GT49 is a cell that I know is blank, or the lowest value I have in the wells. This could be a different value for you, so make sure you pick the right cell. The reason we do this is because this is the way that we normalize the data that we have against the blank. Now your number for cell B2 should be different. Now click on the little box on the right hand corner of cell B2 and drag it all the way across your entire set of data. Now all of your numbers should be normalized to the blank. Now boot up your Microsoft Excel. Copy everything you had from Sheet2 and paste it into Microsoft Excel. Then save it as a CSV (Comma-delimited) file. You should be able to do this in LibreOffice as well but I think there is some tiny formatting detail that YODA can see differently between the two. If you don't have access to Excel ask someone, and long term we should figure out how to get this to work with LibreOffice. Now go to this website in order to access YODA. Click on "Upload" on the left-hand side of the web page. Fill out the "Name" with the name of your experiment, and a brief description if you want (the description part is optional). The only thing you really want to do in this page is scroll all the way down and upload your saved CSV file. Before you do that though, make sure that you remove the other days, if they are not necessary. You can do this by clicking "remove". Note that if you had a YODA login, it will keep tabs on all of your experiments. If you don't, then the experiment will disappear once you clear your cookies. Find the CSV file and make sure to change the "Background" to "value" and change the value in the box to "0.00". It will give you a warning message saying that about the value, but ignore it. Then click on the "Manage" link on the left hand side of the web page, then click on "Edit". Again, change the value of the background to 0.00 and click update. You should get two check marks if you did this correctly. From here, click on the "Export" link and select your experiment, and the "Runs" and "Wells" should automatically show. Click on "Export" from here and save the file. You should now have a file that states the doubling time for all of your samples. The first thing I would do from here is make sure that everything is saved, and to label which sample and condition is in which well.